5. CONCLUSIONS
To our knowledge, this is the first genome-wide study investigating both population genomics and bacterial communities associated with Ceratitis capitata.  Our data offer an in-depth view of medfly population structure and yields insights into the influence of invasion pathways on the microbial diversity. It revealed genetic structure, with one genetic cluster in South Africa (the native range of medfly), and then two distinct genetic clusters in the introduced range: one associated to the Brazilian individuals and the other, clustering specimens further distance such as Spain, Greece, Guatemala, and Australia. Furthermore, the microbiome surveys highlighted Brazil as the most diverse set of microbiota compared with all other sampling sites.
Both approaches (genomic and microbiome) emphasize the uniqueness of Brazil’s population, which opens the possibility for a completely independent colonisation route from Africa to America during the colonial period, using the transatlantic trade routes that passed through St. Helena Island. Museum records and ABC modelling with supervised machine learning supported this alternative colonisation route. In any case, further research is needed to elucidate the possible effect of microbiota in the genomic divergence at a population level and to identify the possible role and transmission pattern of the microbiome in the host fly.
Worldwide medfly management requires huge financial resources. The use of genomic tools provides an opportunity to develop a framework for a survey of medfly invasion pathways and to identify alleles that might be crucial for population differentiation. We suggest that future studies should use SNPs information to create quick identification methods (e.g., genomic tagging) that will help to inform potential novel outbreaks to the quarantine services and allow for better development and implementation of suitable pest management strategies.